Here's the problem: the FP is explicitly instructing its members on what position to take on a political issue.
Correct.
What happens if a member takes a contrary view, and the Church finds out about it -- will that member be disciplined for going contrary to an explicit FP instruction? With this latest letter, is it even possible for a faithful member to put a "NO to the gay marriage amendment" in his/her front yard, or will that be considered public opposition to the Brethren, and grounds for discipline?
Should be. But if Harry Reid can get away with bashing the Church, standing in the same city on the same day as LDS officials there to support the marriage amendment, without censure, then perhaps so can everyone else.